Handbrake is great if you want to do transcoding, but all he wants to do is change the container. When you can do that with the tool posted on the last page without any quality loss or CPU power then why would you even bother transcoding it with Handbrake?

If you want to rip a high-quality source or transcode to smaller sizes etc then Handbrake is indeed the only tool you should even consider using.

I'm using XenonMKV (http://xenonmkv.ev98.net/) to convert a batch of MKVs to my new Nexus 7 - have been using it for ages, back when I had a BlackBerry Playbook. It keeps the video track intact, and re-encodes the audio to AAC.